biology/bowtie has the following bit # FIXME: bowtie-align intermittently dumps core when compiled with clang # GCC 4.2 does not provide good performance USE_GCC= yes alas it now fails to build with GCC 8, blocking the update of the default version of GCC. Cf. http://package22.nyi.freebsd.org/data/112amd64-default-PR231590/2018-10-29_06h48m05s/logs/errors/bowtie-1.1.2_6.log ebwt.h: In member function 'uint32_t* Ebwt<TStr>::isa() const': ebwt.h:863:44: error: cannot convert 'TIndexOffU* const' {aka 'long unsigned int* const'} to 'uint32_t*' {aka 'unsigned int*'} in return uint32_t* isa() const { return _isa; } /* check */ ^~~~ How about retiring this port in favor of biology/bowtie2 ?
We generally want to avoid removing scientific ports unless they become very difficult to maintain, since researchers may need to reproduce results years after the initial analysis, e.g. for grant renewals. There's a simple workaround for this one, which I'll commit shortly,
A commit references this bug: Author: jwb Date: Sat Nov 3 23:24:30 UTC 2018 New revision: 483954 URL: https://svnweb.freebsd.org/changeset/ports/483954 Log: biology/bowtie: Patch for gcc8 and clean up PR: 232929 Reported by: gerald Approved by: jrm (mentor, implicit) Changes: head/biology/bowtie/Makefile head/biology/bowtie/files/patch-ebwt.h
(In reply to Jason W. Bacon from comment #1) > We generally want to avoid removing scientific ports unless they become > very difficult to maintain, since researchers may need to reproduce results > years after the initial analysis, e.g. for grant renewals. There's a simple > workaround for this one, which I'll commit shortly, Thank you, Jason! That was quick. :-) And the explanation on keeping the original version of bowtie in addition to bowtie2 does make sense. (You haven't closed the PR yet, so I'll just move it to "In Progress" based on your commit.)
Tested with USE_GCC=8. Should be OK now.